9DO2 | pdb_00009do2

#1664 Fab in complex with NG2 COBRA hemagglutinin

PDB DOI: https://doi.org/10.2210/pdb9DO2/pdb
EM Map EMD-47071: EMDB EMDataResource

Classification: VIRAL PROTEIN/Immune System
Organism(s): Homo sapiens, Influenza A virus
Expression System: Homo sapiens
Mutation(s): No

Deposited: 2024-09-18 Released: 2025-07-30
Deposition Author(s): Nagashima, K., Mousa, J.
Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.45 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

This is version 1.0 of the entry. See complete history.

Literature

#1664 Fab in complex with NG2 COBRA hemagglutinin

Nagashima, K., Mousa, J.

To be published.

Macromolecule Content

Total Structure Weight: 228.27 kDa
Atom Count: 9,327
Modeled Residue Count: 1,109
Deposited Residue Count: 1,956
Unique protein chains: 3

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Fab-1664 heavy chain	A [auth H]	127	Homo sapiens	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

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Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Fab-1664 light chain	B [auth L]	110	Homo sapiens	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
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Reference Sequence

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Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Hemagglutinin	C [auth A], D [auth B], E [auth C]	573	Influenza A virus	Mutation(s): 0 Gene Names: HA
UniProt
Find proteins for A0A5B8WJL2 (Influenza A virus) Explore A0A5B8WJL2 Go to UniProtKB: A0A5B8WJL2
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A5B8WJL2
Glycosylation
Glycosylation Sites: 8	Glycosylation Focus chain C [auth A] Focus chain D [auth B] Focus chain E [auth C]
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

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Entity ID: 4
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	F [auth D], G [auth E], I [auth G], J [auth I], K [auth J], F [auth D], G [auth E], I [auth G], J [auth I], K [auth J], L [auth K], N, O, P, Q, S, T	2		N-Glycosylation	Interactions Focus chain F [auth D] Focus chain G [auth E] Focus chain I [auth G] Focus chain J [auth I] Focus chain K [auth J] Focus chain L [auth K] Focus chain N Focus chain O Focus chain P Focus chain Q Focus chain S Focus chain T Interactions & Density Focus chain F [auth D] Focus chain G [auth E] Focus chain I [auth G] Focus chain J [auth I] Focus chain K [auth J] Focus chain L [auth K] Focus chain N Focus chain O Focus chain P Focus chain Q Focus chain S Focus chain T
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Entity ID: 5
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	H [auth F], M	3		N-Glycosylation	Interactions Focus chain H [auth F] Focus chain M Interactions & Density Focus chain H [auth F] Focus chain M
Glycosylation Resources
GlyTouCan: G15407YE GlyCosmos: G15407YE GlyGen: G15407YE

Entity ID: 6
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	R	7		N-Glycosylation	Interactions Focus chain R Interactions & Density Focus chain R
Glycosylation Resources
GlyTouCan: G46836GH GlyCosmos: G46836GH GlyGen: G46836GH

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAG (Subject of Investigation/LOI) Query on NAG Download Ideal Coordinates CCD File SDF format, chain AA [auth C] SDF format, chain BA [auth C] SDF format, chain U [auth A] SDF format, chain W [auth A] SDF format, chain Z [auth B] SDF format, chain Y [auth B] SDF format, chain X [auth B] SDF format, chain V [auth A] MOL2 format, chain AA [auth C] MOL2 format, chain BA [auth C] MOL2 format, chain U [auth A] MOL2 format, chain W [auth A] MOL2 format, chain Z [auth B] MOL2 format, chain Y [auth B] MOL2 format, chain X [auth B] MOL2 format, chain V [auth A] mmCIF format, chain AA [auth C] mmCIF format, chain BA [auth C] mmCIF format, chain U [auth A] mmCIF format, chain W [auth A] mmCIF format, chain Z [auth B] mmCIF format, chain Y [auth B] mmCIF format, chain X [auth B] mmCIF format, chain V [auth A]	AA [auth C] BA [auth C] U [auth A] V [auth A] W [auth A] AA [auth C], BA [auth C], U [auth A], V [auth A], W [auth A], X [auth B], Y [auth B], Z [auth B]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain AA [auth C] Focus chain BA [auth C] Focus chain U [auth A] Focus chain V [auth A] Focus chain W [auth A] Focus chain X [auth B] Focus chain Y [auth B] Focus chain Z [auth B] Interactions & Density Focus chain AA [auth C] Focus chain BA [auth C] Focus chain U [auth A] Focus chain V [auth A] Focus chain W [auth A] Focus chain X [auth B] Focus chain Y [auth B] Focus chain Z [auth B]